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combofix download stopped my card reader

This is my first post, so if I'm in the wrong place please advise. A few days ago I downloaded and ran combofix at the advice of a friend. My system seemed stable, but I wanted to check for hidden malware. It turned up a dozen or so suspicious files and quarantined them. But after that, when I insert an SD card into my usb reader, the auto transfer wizard does not start. Can't get it to work. I did a system restore and was able to manually remove all the malware except one hidden registry setting. Then it took me 2 days to download combofix again (!! 404 errors galore). This time I noticed that the card reader function was gone even before running combofix. Just downloading it to my desktop killed the app. Anyone know of a fix?